The serial is set on the Earth colony world Terra Alpha. In the serial, the alien time traveller the Seventh Doctor (Sylvester McCoy) starts a rebellion against the planet's ruler, Helen A (Sheila Hancock), a woman who seeks to eliminate all unhappiness on the planet.

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The Seventh Doctor and Ace visit a human colony on the planet Terra Alpha, where the planet's secret police force, the Happiness Patrol, roam the streets hunting down and killing so-called 'Killjoys'. The colony is governed by Helen A, who is obsessed with eliminating unhappiness. Also in her employee is the Kandy Man, a grotesque, sweet-based robot created by Gilbert M, one of Helen A’s senior advisers.

The Doctor and Ace meet an unhappy guard Susan Q, who becomes an ally, and Earl Sigma, a wandering harmonica player. They, along with the native inhabitants of Terra Alpha, the Pipe People, work to overthrow the tyranny of Helen A. They begin supporting public demonstrations of unhappiness, encouraging the people to revolt, and attempting to expose Helen A's population control programme to Trevor Sigma, an official galactic census taker.

The first to be disposed of is Helen A’s pet Stigorax, Fifi, a rat-dog creature used to hunt down the Pipe People, as it is crushed in the pipes below the city when Earl causes an avalanche of crystallised sugar with his harmonica. Then the Pipe People destroy the Kandy Man in a flow of his own fondant surprise (previously used to execute dissidents). Realising that she is beaten, Helen A attempts to escape the planet in a rocket, only to discover that the rocket has already been commandeered by Gilbert M and Joseph C, her husband. She tries to flee, but the Doctor stops her, and tries to teach her about the true nature of happiness, which can only be understood if counterbalanced by sadness. Helen A at first sneers at the Doctor, but when she discovers the remains of her beloved pet Fifi, she collapses in tears, and finally feels some sadness of her own.

Working titles for this story included The Crooked Smile.[2] The production team considered transmitting this story in black and white to fit with its intended film noir atmosphere.[2] A fan myth holds that the third episode was supposed to be animated, but this was never the case.[3] The entire serial was shot in studio in July and August 1988.[4]

Helen A was intended to be a caricature of then British Prime Minister Margaret Thatcher.[5] Hancock stated that she "hate[d] Mrs Thatcher with a deep and venomous passion".[4] In 2010, Sylvester McCoy told the Sunday Times: "Our feeling was that Margaret Thatcher was far more terrifying than any monster the Doctor had encountered". The Doctor's calls on the drones to down their tools and revolt was intended as a reference to the 1984-1985 miners' strike.[5] Most of this element was eventually toned down.[2]

Ian Berriman of SFX wrote that The Happiness Patrol was "far superior" to Dragonfire, particularly praising the Kandyman and the supporting cast. However, he felt that "while the script is brimming with witty, provocative ideas and droll one-liners, it struggles to piece them together into a satisfying narrative".[10]Radio Times reviewer Patrick Mulkern described it as a "clever and funny satire" and praised the acting and political commentary.[4]DVD Talk's John Sinnott gave The Happiness Patrol five out of five stars, calling it a "minor masterpiece". He commended the irony, social commentary, and McCoy's acting.[11]

A novelisation of this serial, written by scriptwriter Graeme Curry, was published by Target Books in February 1990. Adapting his scripts rather than the televised version, Curry's book includes scenes cut during editing and his original envisioning of the Kandy Man with a human appearance, albeit with powdery white skin and edible candy-cane glasses. An unabridged reading of the novelisation by Rula Lenska was released by BBC Audiobooks in July 2009.